dot-create_list_with_template: Create list and substitute substrates/products

In michaelwitting/wormLipidPredictR: Lipid reaction prediction based on WormJam

Create list and substitute substrates/products

Description

Helper function for create_reaction.

The function .create_list_with_template takes the template and replaces the "reactionFormula" by the substrates/products from df_reaction.

Usage

.create_list_with_template(df_reaction, template, reaction = "RHEA:15421")

Arguments

df_reaction	data.frame
template	list
reaction	character(1)

Details

The string replacement depend on the reaction argument.

Value

list

Author(s)

Michael Witting, [e-mail] and Thomas Naake, [e-mail]

Examples

FA <- c("FA 14:0(12Me)", "FA 16:0(14Me)", "FA 15:1(9Z)(14Me)",        
    "FA 17:0(16Me)", "FA 12:0(11Me)", "FA 13:0(12Me)", "FA 14:0(13Me)",
    "FA 15:0(14Me)", "FA 16:0(15Me)", "FA 12:0", "FA 14:0")
substrates <- list(FA = FA)
reaction <- "RHEA:15421"

## create template
template <- LipidNetworkPredictR:::.create_template(template = NA, 
    reaction = reaction)

## create data.frame of substrates
df_substrates <- LipidNetworkPredictR:::.create_substrates_combinations(
    substrates = substrates, template = template)
    
## add products to data.frame
df_reaction <- LipidNetworkPredictR:::.add_products(
    substrates = df_substrates, 
    reaction = reaction)
    
## make new data.frame with reaction template
LipidNetworkPredictR:::.create_list_with_template(
    df_reaction = df_reaction,
    template = template, reaction = reaction)

michaelwitting/wormLipidPredictR documentation built on Feb. 28, 2025, 5:02 a.m.